In regards to the warning "We are currently unaware of what BlackCipher does." if this is a literal statement then I found a post that explains what Black Cipher is. As everyone probably initially expected, Black Cipher is security software.
http://mabinogi.nexon.net/News/All/27/00G9y/introducing-black-cipherHowever, Nexon's post might be a bit misleading so I wanted to clarify a few things. I do apologize if the following has been stated in prior post by someone else.
Black Cipher Security is a company that offers network security programs to businesses. They don't offer very specific information about their products but with what information they do give, and the lack of evidence to say otherwise, I feel confident that BC's primary concern is protecting the integrity of servers, that is to say; protection against server-sided hacks. I feel like it might protect against some forms of datamining as well but I'm not 100% sure. BCS does claim they can offer a security program for any need so Nexon could at any time say that they want to prevent the game from being modable and BCS would probably acquiesce but, seeing as modded versions of the game run fine, I do not believe this has yet been done.
Interestingly enough it seems like Black Cipher is using AES encryption for themselves. For those who don't know; AES is one of the most widely used forms of encryption to prevent a file from being opened and read or altered by unauthorized users. Why this is interesting to me is; if Black Cipher is so much more innovative with their security than larger companies, why aren't they using a more updated cipher such as XTEA or TwoFish which have not had any publicly proven cracks (that I'm aware of at least). Then again, the files found in the mabinogi folder might not contain particularly sensitive information, who knows?
Anyway, as it stands I do not feel that Black Cipher is something the average mod user should be concerned about right at this moment, however mod builders might want to use caution and it should be noted that Black Cipher can change with any update without warning.